in-silico prediction of structural and functional aspects of a hypothetical protein of Arabidopsis thaliana (L) Heynh.

Abstract

Arabidopsis thaliana is a model plant for scientific research due to the presence of many desirable characteristics like rapid development, small plant size, mutable seeds, mutations quickly becoming homozygous etc. An in-silico technique was initiated to characterize a hypothetical protein to deduce its structural and functional information. The hypothetical protein analysed in the present study showed domain characteristics of ankyrin repeats family with beta-hairpin-alpha-hairpin repeat {multiple repeats of beta (2) - alpha (2) motif}. The protein showed five domains of 32 amino acid repeat units. The modelled protein revealed the presence of maximum number of random coils as its secondary structural elements. The existence of ankyrin repeats indicates its role in protein-protein interaction essential for various metabolic processes in organism.

Keywords: Arabidopsis thaliana; hypothetical protein, ankyrin repeats, protein-protein interaction.

Introduction

Arabidopsis thaliana (L) Heynh. is a small flowering plant that is widely used as a model organism [1] in plant biology. It has a small genome of about 125 Mb organized into five chromosomes and contains an estimated 25,500 genes. More than 30 megabases of annotated genomic sequence has already been deposited in GenBank by a consortium of laboratories in Europe, Japan, and the United States. The entire genome has been sequenced which has enhanced the importance of Arabidopsis as a model for plant biology. Its genome was sequenced in the year 2000. Most of the DNA encodes 25,498 genes and very little junk DNA is present. Many characters of this unique plant such as prolific seed production, rapid development, small plant size, mutable seeds, normally self pollinated thereby making mutations quickly becoming homozygous and its expression, make it an ideal model organism for scientific research.

The large scale genome sequencing project has generated a plethora of information both in terms of genes and proteins. There are however, a vast amount of proteins whose function and structure has not been unearthed yet. There is, therefore, an urgent need to characterize these hypothetical proteins whose only primary information in the form of sequence is available. The results generated will be helpful in gaining insight into the various metabolic, gene regulatory mechanism and the functional aspects of this unique model organism. Therefore, the present work involves the extensive use of tools and graphical software for a complete annotation of the hypothetical protein (Acc. No. gi|4206201|gb|AAD11589.1|).

About the Authors:

A .Bhattacharjee and S. R. Joshi
Department of Biotechnology & Bioinformatics,
School of Life Sciences, North Eastern Hill University,
Shillong -793 022, Meghalaya, INDIA.

H .Choudhury
Department of Basic Sciences & Social Sciences, School of Technology
North Eastern Hill University,
Shillong -793 022, Meghalaya, INDIA.

U. Maheswari
St. Aloysius College, Karangalpady, Mangalore -575 003, Karnataka, INDIA.

For correspondence

A .Bhattacharjee
E-mail: atanubio@gmail.com;
Tel:+91 0364 2722406;
Fax: +91 0364 2550076

  

 

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